groovy & grails - lecture 10

Groovy: Efficiency Oriented ProgrammingLecture 10

Master Proteomics & Bioinformatics - University of GenevaAlexandre Masselot - summer 2011

Agenda

‣SVN & google code hosting

‣More on GSP

‣ Including third parties libraries

‣Ajax

‣Runtime environment

‣Domains

‣Code evolve in time

‣Source code is shared

‣Source Code Management system host code + versioning

‣Many solutions exist: CVS, SVN, GIT, SourceSafe...

‣SVN is a client/server solution

‣Server can be in-house

‣Free solution for open source

http://code.google.com/hosting/

make an google account

Create ProjectProject name: geop-demo

Project summary: A demo project for GEOP course

Project description: geop demo code Version control system: Subversion Source code license: New BSD License Use a separate content license:license...

Project labels:

Create project...

Project name must start with a lowercase letter, followed by lowercase letters, digits, and dashes, with no spaces. This will be part of your project's URL and cannot be changed later.Project summary will be shown whenever the project's name is displayed.Project description is the main content of your project's home page. You may use wiki markup.Version control system selects the type of your project's repository. Learn more.Licenses determine how others may build upon your work. Code and documentation may be distributed under separate licenses.Project labels help classify your project so others can easily find it or browse projects by label.

Google proposes command line commandsWe’ll see how to integrate svn into eclipse

Command-line access

If you plan to make changes, use this command to check out the code as yourself using HTTPS:

# Project members authenticate over HTTPS to allow committing changes.svn checkout https://geop-demo.googlecode.com/svn/trunk/ geop-demo --username alexandre.masselot

When prompted, enter your generated googlecode.com password.

Use this command to anonymously check out the latest project source code:

# Non-members may check out a read-only working copy anonymously over HTTP.svn checkout http://geop-demo.googlecode.com/svn/trunk/ geop-demo-read-only

GUI and IDE access

This project's Subversion repository may be accessed using many different client programs and plug-ins. See your client's documentation for more information.

Google code offers for “free”

‣SVN repository

‣Managing contributors to a project

‣SVN repository

‣Wiki

‣SVN repository

‣Wiki

‣Ticketing system

‣SVN repository

‣Wiki

‣Ticketing system

‣Bug reporting

‣SVN repository

‣Wiki

‣Ticketing system

‣Bug reporting

‣Visibility

Google code hosting⇒

your code is open source

SVN: eclipse or command line

Installing svn in Eclipse

‣Help > dashboard > extension- Subversion (subclipse)

Installing svn in Eclipse

‣Help > dashboard > extension- Subversion (subclipse)

‣Or command line: installed by default or- sudo apt-get install subversion

Eclipse: connecting to the SVN repository

‣menu Window - > open perspective

- > SVN repository exploring

Eclipse: connecting to the SVN repository

‣menu Window - > open perspective

- > SVN repository exploring

‣view SVN repositories- > right click

- > new repository location

- https://geop-demo.googlecode.com/svn

Sharing an existing project to your google code account

‣Perspective java

Sharing an existing project to your google code account

‣Perspective java

‣project right-click- > team

- > share project- use specifier folder name

trunk/your.project.name

‣username & password

from google page

‣save password

check box

Commit the project

‣At this stage, the project is only created on the remote server- check with SVN repository exploring perspective- or browse source code from google page

Commit the project

‣Mark generated file & folder to be ignored from svn- e.g. target/

Commit the project

‣Mark generated file & folder to be ignored from svn- e.g. target/

‣Right-click > team > add to svn:ignore

All eclipse functionalitiescan be replaced by shell commands

SVN command line: share project

‣ Import original project demo.svn to the repository

‣cd workspace directorysvn import -m “initial import” --non-recursive demo.svn https://geop-demo.googlecode.com/svn/trunk/demo.svn

‣Directory itself is not imported, so checkout (with force)svn checkout --force https://geop-demo.googlecode.com/svn/trunk/demo.svn

SVN command line: share project (cont’d)

cd demo.svn

‣Add target/ directory to svn:ignoresvn propset svn:ignore target .

‣Add other directories to svnsvn add $(ls | grep -v target)

‣Commit filessvn commit -m "adding all initial files"

‣Back to eclipse, F5 (refresh in package explorer view)

Browse your project

From google code source page

SVN for a daily use

SVN for a daily useSVN for a daily useminutely

SVN: flow use

‣Checkout out or share an existing project to contribute

SVN: flow use

‣Commit changes to the repository

SVN: flow use

‣Update changes from repository

SVN: flow use

‣Update changes from repository

‣Eclipse: - select project- > right-click - > team- > Synchronize with repository- commit/update/manage conflict

SVN: flow use (cont’d)

‣Command linesvn statussvn updatesvn commit -m “my message to describe changes”

Commit/update often

SVN is more

‣History

SVN is more

‣History

‣See contribution from others

SVN is more

‣History

‣Tag / branch versions

SVN is more

‣History

‣Conflict resolution

SVN is more

‣History

‣Continuous integration / testing on dedicated server

SVN is more

‣History

‣File locking :(

SVN is more

‣History

‣File locking :(

‣ Integration with tickets

SVN is more

‣History

‣File locking :(

‣ Integration with tickets

‣Windows integration: http://tortoisesvn.tigris.org/

Back to grails... and proteins isoforms

Problem: uniprot AC ➙ isoform listin a web application

Grails: including a third parties libraries

‣Library is available as a jar (export ➙ .jar)

‣Copy jar in lib/

‣For eclipse completion- right-click- build path- add to build path

Get is forms for ac (00:44:01.975)Q70Z44List

>Q70Z44-1MQKHSPGPPALALLSQSLLTTGNGDTLIINCPGFGQHRVDPAAFQAVFDRKAIGPVTNYSVATHVNISFTLSAIWNCYSRIHTFNCHHARPWHNQFVQWNPDECGGIKKSGMATENLWLSDVFIEESVDQTPAGLMASMSIVKATSNTISQCGWSASANWTPSISPSMDRARAWRRMSRSFQIHHRTSFRTRREWVLLGIQKRTIKVTVATNQYEQAIFHVAIRRRCRPSPYVVNFLVPSGILIAIDALSFYLPLESGNCAPFKMTVLLGYSVFLLMMNDLLPATSTSSHASLVAPLALMQTPLPAGVYFALCLSLMVGSLLETIFITHLLHVATTQPLPLPRWLHSLLLHCTGQGRCCPTAPQKGNKGPGLTPTHLPGVKEPEVSAGQMPGPGEAELTGGSEWTRAQREHEAQKQHSVELWVQFSHAMDALLFRLYLLFMASSIITVICLWNT

>Q70Z44-2MASMSIVKATSNTISQCGWSASANWTPSISPSMDRAERSPSALSPTQVAIRRRCRPSPYVVNFLVPSGILIAIDALSFYLPLESGNCAPFKMTVLLGYSVFLLMMNDLLPATSTSSHASLVRPHPSRDQKRGVYFALCLSLMVGSLLETIFITHLLHVATTQPLPLPRWLHSLLLHCTGQGRCCPTAPQKGNKGPGLTPTHLPGVKEPEVSAGQMPGPGEAELTGGSEWTRAQREHEAQKQHSVELWVQFSHAMDALLFRLYLLFMASSIITVICLWNT

Isoforms_v1 -> v5 same controllerdifferent views (gsp)

for different rendering interaction

Isoforms_v1 -> v5 same controllerdifferent views (gsp)

for different rendering interaction

Isoforms_vXController⇒

views/isoforms_vX/ direcgtory with gsp’s

IsoformController_v?.groovy

def list = { def ac=params.ac def xml=new XmlSlurper() .parseText("http://pir.uniprot.org/uniprot/${ac}.xml".toURL().text).entry UniprotEntrySplicer splicer=[entryXml:xml] def proteins=splicer.buildAllIsoforms().values() as List

[proteins: proteins] }

isoforms_v1/list.gsp

<html> <body> <h2>Get is forms for ac (${String.format('%tH:%<tM:%<tS.%<tL', new Date())})</h2> <g:form action="list"> <g:textField name="ac" value="${params.ac}" /> <g:submitButton name="submit" /> </g:form> <h3>List</h3> <g:each in="${proteins}" var="prot"> <pre> ${prot} </pre> </g:each> </body></html>

Problem: direct access to /list only

isoforms_v2: add index.gsp

<html> <body> <h1>Isoform list application</h1> <h2>Get is forms for ac (${String.format('%tH:%<tM:%<tS.%<tL', new Date())})</h2> <g:form action="list"> <g:textField name="ac" value="${params.ac}" /> <g:submitButton name="submit" /> </g:form> </body></html>

Problem: <g:form> is duplicated (DRY!)

isoform_v3: use template

‣_form.gsp<h2>Get is forms for ac (${String.format('%tH:%<tM:%<tS.%<tL', new Date())})</h2><g:form action="list"> <g:textField name="ac" value="${params.ac}" /> <g:submitButton name="submit" /></g:form>

‣ In index.gsp and list.gsp <g:render template="form" />

Problem: all the page is reloaded totally

Ajax: asynchronous load

Q70Z44

web browser

submit

isoform/list

server

Q70Z44

web browser

submit

isoform/list

server

Q70Z44

>Q70Z44-1MQKHSPGPPALALLSQSLLTTGNGDTLIINCPGFGQHRVDPAAFQAVFDRKAIGPVTNYSVATHVNISFTLSAIWNCYSRIHTFNCHHARPWHNQFVQWNPDECGGIKKSGMATENLWLSDVFIEESVDQTPAGLMASMSIVKATSNTISQCGWSASANWTPSISPSMDRARAWRRMSRSFQIHHRTSFRTRREWVLLGIQKRTIKVTVATNQYEQAIFHVAIRRRCRPSPYVVNFLVPSGILIAIDALSFYLPLESGNCAPFKMTVLLGYSVFLLMMNDLLPATSTSSHASLVAPLALMQTPLPAGVYFALCLSLMVGSLLETIFITHLLHVATTQPLPLPRWLHSLLLHCTGQGRCCPTAPQKGNKGPGLTPTHLPGVKEPEVSAGQMPGPGEAELTGGSEWTRAQREHEAQKQHSVELWVQFSHAMDALLFRLYLLFMASSIITVICLWNT >Q70Z44-2MASMSIVKATSNTISQCGWSASANWTPSISPSMDRAERSPSALSPTQVAIRRRCRPSPYVVNFLVPSGILIAIDALSFYLPLESGNCAPFKMTVLLGYSVFLLMMNDLLPATSTSSHASLVRPHPSRDQKRGVYFALCLSLMVGSLLETIFITHLLHVATTQPLPLPRWLHSLLLHCTGQGRCCPTAPQKGNKGPGLTPTHLPGVKEPEVSAGQMPGPGEAELTGGSEWTRAQREHEAQKQHSVELWVQFSHAMDALLFRLYLLFMASSIITVICLWNT

web browser

submit

isoform/list

server

isoform_v4/index.gsp

<html> <head> <g:javascript library="prototype" /> </head> <body> <h2>Get is forms for ac (${String.format('%tH:%<tM:%<tS.%<tL', new Date())})</h2>  <g:formRemote name="listForm" url="[action:'list']" update="isoforms-list"> <g:textField name="ac" value="${params.ac}" /> <g:submitButton name="submit" /> </g:formRemote>  <div id="isoforms-list"/> </body></html>

isoform_v4/list.gsp

Twitter 1

People post messages and follow others

database (domain)+ controller (actions)

+ views (web)

Domain: Person & Message

Domain: bean definition + database storage

Person domain

‣Create the database entry + bean class grails create-domain-class Personproject > right-click > grails > create-domain-class Person

Person domain

‣Create the database entry + bean class grails create-domain-class Personproject > right-click > grails > create-domain-class Person

‣Files created:./grails-app/domain/eop/lec10/twitter/Person.groovy./test/unit/eop/lec10/twitter/PersonTests.groovy

Person.groovy

‣Created classpackage eop.lec10.twitter

class Person {

static constraints = { }}

Person.groovy

‣Enriched with fieldspackage eop.lec10.twitter

class Person { String username String firstName String lastName String email Date dateCreated

static constraints = { }}

run-app ⇒ database + table created

Web access: need controller + views

Scaffolding is pure magic

PersonController.groovy

create-controller Person

‣grails-app/controller/PersonController.groovy:package eop.lec10.twitter

class PersonController { def scaffold = true}

‣scaffold generate all default action & view implicitely

http://localhost:8080/eop.lec10.twitter/person

‣Default url is redirected on the list page

‣Entering a new Person lucky luke

‣Back to list- view all- edit- delete- sort

Domain constraints

Person.groovy

class Person { String username String firstName String lastName String email Date dateCreated

//firstName is compulsory //email field has an email format //username cannot be null, is unique and is between 6 and 20 characters static constraints = { firstName(blank:false) email(email:true, blank:false) username(blank:false, unique:true, matches:/\w{6,20}/) }}

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